Figure A1:

The behavior of the LD contribution (y-axis) to the genetic variance (red) and the Haseman-Elston regression estimate (blue) as a function of LD, i.e. $\mathbb{C}\left(z_i,z_j\right)$ (x-axis). Each point represents the contribution calculated from a random draw of genotypes, given $\mathbb{C}\left(z_i,z_j\right)\propto (f_{\mathrm{i}}^{\mathrm{A}}-f_{\mathrm{i}}^{\mathrm{B}})(f_{\mathrm{j}}^{\mathrm{A}}-f_{\mathrm{j}}^{\mathrm{B}})$. The red line represents the expected LD contribution and the black dashed line represents the contribution expected in the case of perfect LD.